SMAP chromplot

This is the manual for the SMAP chromplot module of the SMAP package.

SMAP chromplot is a module that visualizes the haplotypes relative to two specific reference samples SMAP delineate.

SMAP chromplot is a useful tool to identify heterozygosity, crossover events, the origin of introgressed segments, etc.

SMAP chromplot can also be used to optimize bioinformatics parameter settings across all steps of read data analysis, including read preprocessing, read mapping (e.g. BWA-MEM), and selection of high quality loci by SMAP delineate.

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Required input
  • Commands & options
  • Example commands
  • Output
• Feature Description
• How It Works
• Examples